A current employee at the site has given The Courier-Mail a detailed account of staff members rorting thousands of dollars from the company.

The source alleged staff were claiming to have worked 12 hours on timesheets, but in reality only worked two hours, and were faking work trips to claim the company's travel allowance.

They also claimed drug use was rampant at the site and that people were sacked, but the problem continues today.

Rail Tram and Bus Union Queensland secretary Owen Doogan.

Queensland Rail chief executive Nick Easy. Pictures: Annette Dew

Queensland Rail chief executive Nick Easy acknowledged three employees were sacked for drug use in the past 12 months and a supervisor was found to be authorising incorrect time sheets.

But Rail Tram and Bus Union Queensland secretary Owen Doogan promptly dismissed any suggestion of an ongoing issue at the Bowen Hills site.

"The whistleblower - I'd like to know who they are," Mr Doogan said.

"It's probably just some disgruntled former employee making things up."

While Mr Doogan acknowledged the dismissal of four people in the past 12 months, he thoughts claims of staff faking work trips in order to claim the company travel expenses were a bridge too far.

"It's absolute nonsense," he said.

A train arrives at Bowen Hills station in Brisbane.

Opposition leader Deb Frecklington yesterday called on the State Government to stand up for commuters.

"These allegations surrounding what's been going on at QR are just disgraceful," she said.

"After a thousand days of QR cancelling all of those train services, now we've got this rot happening. Where is the minister, where is the premier? Why don't they ever stand up for the commuters of Brisbane?"

A State Government spokesman said: "If anyone has any evidence to support any allegation, they should make the appropriate referrals so it can be properly investigated."